The water taxis in Annapolis are not
free! If I recall correctly, its anywhere from $2 - $6 per person each way? The water taxis monitor channel 68, water taxi website: http://www.watermarkcruises.com/watertaxi.htm
Most probably use the dingy dock at the end of "Ego Alley". BTW, you didn't mention if you have a dingy?
A mooring will run you about $25.00 for the night, with access to the Harbor Master Bath & Shower facility. Most likely you will want to pick up the first mooring you see, and of its hot I recommend one before the bridge. You would also not have to deal wit the bridge openings (every 1/2 hour btw) The wakes usually settle down at dusk.
FWIW, we did about a 90 mile run a few years ago from St Marys (Horseshoe Bay) to St. Michaels in about 14 hours. We left about 05:30 and dropped the hook around 19:30 averaging about 6.5 knts...which included motoring sailing for a couple of hours in the mid afternoon. But weather was optimal for the most part.